PathoDB® Release 2.0 - Documentation

Mutated Site : Fields

AC

Accession Number

accession number of the mutated site

ID

Identifier

{species acronym $ {gene acronym}

DT

Date

creation date; author

DT

Date

date of last update; updater

SC

Site Source

g (DNA) or r (RNA)

OS

Species

biological species (TRANSFAC®)

OC

Taxonomic Classification

systematic biological classification of the species (TRANSFAC®)

SO

Factor Source

link to cells/expression systems the binding factors were derived from; cell name

DE

Description

link to TRANSFAC® Gene (via accession number); gene name

RE

Site Region

functional region of the gene (e. g. promoter, enhancer, intron etc.) where the mutated site is located

EL

Element

specific term for a particular site (e.g. estrogen response element, Sp1 site)

WS

Wildtype Site

link to wildtype site (via accession number); wild type site identifier; gene name

MS

Mutated Sequence

mutated sequence; either corresponding to the linked TRANSFAC® site sequence or a DNA stretch of >= 20 nucleotides (enclosing the mutation). When the authors emphasized a certain sequence motif within a sequence, it is written in capitals, while the rest of the sequence is shown in lowercase letters.

SF

First Position of Element

first position of the mutated site bound by transription factor

ST

Last Position of Element

last position of the mutated site bound by transription factor

S1

Definition of First Position

definition of position numbering (if not referring to the transcription start site) such as ATG or restriction sites

BF

Binding Factor

link to binding wildtype factor (via accession number). The "Quality" of the factor-site interaction is indicated on a six-level scale ->; the alterations in "Binding" of the mutated factor to the wildtype site is indicated on a five-level scale ->

CC

Comment

functional consequences of the mutation in the site are listed here, such as altered factor binding or promoter activity

GT

Genotype

link to the Genotype -> table (via accession number)

MM

Methods

method(s) applied for the identification/characterization of the mutated site

DR

External Databases

link to external database (EMBL) (via accession number)

RN

Reference Number

RX

Reference MEDLINE ID

RA

Reference Author(s)

RT

Reference Title

RL

Reference Journal

 

 

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